Contents

Motivation

A hybrid system is a dynamic system that exhibits both continuous and discrete dynamic behavior,
that is, a system that can both flow (as described by a differential equation) and jump (as
described by a difference equation or a control graph). The continuous-discrete duality is a
phenomenon that occurs naturally in many application areas such as real-time software, embedded
systems, robotics, mechatronics, aeronautics, process control and biological systems. The course
will cover the state-of-the-art modeling, design and analysis of hybrid systems. The main emphasis
will be on biological systems, in particular on engineering genetic circuits.

Objectives

By the end of this course the students will be provided with detailed knowledge and substantial
experience in the mathematical modeling, simulation and verification of hybrid systems, in particular of genetic circuits.

Prerequisites

CSE 214, CSE 220, and CSE 303 are relevant but not required.

Overview

After a brief introduction to the biology of genetic circuits, we will discuss the theoretical
aspects of modeling, simulating and verifying genetic circuits. In the projects, you will then
apply the theory you have learned in the class. The course structure is summarized below:

Reading

Software

The homeworks are going to use the tools to be announced soon.

Communication

In order to exchange ideas and experience with each other, you may want to use the news group
created specially for cse510. To subscribe to this group, proceed as follows (e.g. with the
netscape browser): (1) right click the news.sunysb.edu, (2) select subscribe to
Newsgroups, (3) choose the search panel and search for sbcs.cse510, (4) select the
sbcs.cse510newsgroup and click on the subscribe button. Now you are ready to send
and retrieve messages.

Grading

Your performance on the projects and homework assignments will determine your final grade.

Your
Rights and Responsibilities

Special Needs

If you have a physical, psychological, medical
or learning disability that may impact on your ability to carry out assigned
course work, you are urged to contact the staff in the Disabled

Because a primary goal of the course is to teach
professionalism, any academic dishonesty will be viewed as evidence that
this goal has not been achieved. Any act of cheating will be treated with
utmost seriousness.

You can discuss the course material with other
students, but not the homework assignments themselves. In effect, you can
discuss the problems but not the solutions. If you help another student
with a homework, use examples that do not resemble those in the homework.
Remember that there are many different ways to solve the same problem;
even solutions with the same central idea can be formulated in many different
ways. Therefore, suspiciously similar homework solutions will be considered
as evidence of disallowed collaboration or copying.

In case you have any questions about whether an
act of collaboration may constitute "cheating", please come and talk to
the instructor beforehand to clarify the issue.

Copying an assignment from another student in
this class or obtaining a solution from some other source will lead to
an automatic F for this course and to a disciplinary action. Allowing another
student to copy one's work will be treated as an act of academic dishonesty,
leading to the same penalty as copying. You should learn how to protect
your data. Failure to do so is also unprofessional and it may expose you
to the danger that someone will copy your homework and will submit it as
his or her own (see above). In this case, you may be given a score of 0
for the assignment in question (and the other party will get an F).

All cases of academic dishonesty will be
reviewed by the Engineeing College's committee (CASA).

Survival Tips

Do not postpone working on assignments. Start
working on programming assignments as soon as they are handed out. Do not
wait till the day before the deadline. You will see that assignments take
much more time when you work on them under pressure, than when you are
more relaxed. Remember that no late submissions are allowed.

Do not postpone working on assignments! This cannot
be understated. Despite the above warning, most students will end up working
only around the deadline. Remember, the homeworks usually take more time
that it initially appears. Furthermore, I expect both the TA and me to
be swamped on the office hours before projects are due. So, you, being
wiser than the rest, should start earlier and beat the rush!